Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.4.16.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17534	0.827
27DAP/17DAP	1.67561	0.526
39DAP/27DAP	0.85254	0.458
41DAP/39DAP	1.09831	0.685
42DAP/41DAP	1.20746	0.871
43DAP/42DAP	1.03191	1
47DAP/43DAP	0.85819	0.546
52DAP/47DAP	1.53416	0.671
57DAP/52DAP	1.27833	0.96

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82188	0.06
17DAP/reference	0.78862	0.035
27DAP/reference	0.96343	0.444
39DAP/reference	0.91127	0.342
41DAP/reference	0.86382	0.039
42DAP/reference	0.81586	0.008
43DAP/reference	0.9503	0.316
47DAP/reference	0.9218	0.032
52DAP/reference	1.10863	0.354
57DAP/reference	1.14389	0.159

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.27477	0.774
27DAP/17DAP	0.94055	0.878
39DAP/27DAP	0.90319	0.52
41DAP/39DAP	1.2033	0.152
42DAP/41DAP	0.8594	0.248
43DAP/42DAP	0.8871	0.351
47DAP/43DAP	0.74188	0.01
52DAP/47DAP	1.16171	0.616
57DAP/52DAP	1.50328	0.179
57DAP/7DAP	1.23735	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.71947	0.1
17DAP/reference	0.78734	0.025
27DAP/reference	0.92542	0.159
39DAP/reference	0.83148	0.021
41DAP/reference	0.70388	0.011
42DAP/reference	0.75923	0.111
43DAP/reference	0.74804	0.038
47DAP/reference	0.7798	0.079
52DAP/reference	0.74381	0.015
57DAP/reference	0.81535	0.026

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86835	0.048
17DAP/reference	0.88061	0.143
27DAP/reference	0.88977	0.134
39DAP/reference	0.94002	0.183
41DAP/reference	0.99469	0.57
42DAP/reference	0.96313	0.433
43DAP/reference	1.11891	0.641
47DAP/reference	1.02488	0.965
52DAP/reference	1.17657	0.092
57DAP/reference	1.06977	0.93

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84359	0.048
17DAP/reference	0.90354	0.281
27DAP/reference	0.84654	0.048
39DAP/reference	0.84627	0.069
41DAP/reference	0.90342	0.185
42DAP/reference	0.88476	0.134
43DAP/reference	0.86196	0.12
47DAP/reference	0.90034	0.089
52DAP/reference	0.73759	0.101
57DAP/reference	1.17093	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08656	1
26DAP/20DAP	0.89816	1
34DAP/26DAP	1.72487	0.819
51DAP/34DAP	1.26856	0.458
52DAP/51DAP	1.69333	0.063
53DAP/52DAP	0.81749	0.498
55DAP/53DAP	0.87772	0.336
57DAP/55DAP	2.13312	0.818
62DAP/57DAP	1.42171	0.622
68DAP/62DAP	1.97004	0.071
68DAP/14DAP	1.43077	0.025

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.83826	0.038

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.02789	0.715
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.33074	0.224
Mature Eggplant/Ripe Tomato	0.74615	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.21764
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.84326
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	1.21137
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.50908	0.321
IL2-6/WTpooled	1.06972	0.395
IL7-5/WTpooled	0.70067	1
IL7-3/WTpooled	0.70042	0.418
IL12-4/WTpooled	0.82555	0.52
IL1-4/WTpooled	1.07768	1
WT/WTpooled	1.01141	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.11943	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04947	0.921
DC3000/delta hrp 6h	1.09394
DC3000/delta hrp 12h	1.03547	1
DC3000/delta hrp 24h	0.94988	0.75

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.30017

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.9071	1
Exp 36h	0.85872	0.749
Exp 60h	0.92112	0.754

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.25539	1
Var 0h	0.83731	0.933
Var 12h I row2-row1	0.94542	0.77
Var 12h NI row2-row1	1.41344	0.34
Var 36h I row2-row1	0.93362	1
Var 36h NI row2-row1	0.81593	0.482
Var 60h I row2-row1	0.83905	0.582
Var 60h NI row2-row1	1.0072	1
Time course 0hI-0hNI	1.10382	0.603
Time course 12hI-12hNI	0.92434	0.268
Time course 36hI-36hNI	0.85865	0.08
Time course 60hI-60hNI	0.93512	0.319

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.13487	0.218
transgenic ySAMdc/azygous control (breaker)	0.90733	0.49
transgenic ySAMdc/azygous control (red)	1.0028	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96218	0.092

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87464	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03332	1
Manapal/WT (break)	0.80234	0.299
Manapal/WT (red)	1.5305	0.137